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“The act of smelling something, anything, is remarkably like the act of thinking. Immediately at the moment of perception, you can feel the mind going to work, sending the odor around from place to place, setting off complex repertories through the brain, polling one center after another for signs of recognition, for old memories and old connection.” – Lewis Thomas

Students experiencing olfactory “thrills” while measuring dissolved oxygen and redox potential of soil microcosms after flooding. The rotten-egg odor was intense in several of these samples.

Incorporating multiple senses into the learning process is a hallmark of experiential learning, and has long been viewed as a successful education strategy. In a classroom setting, combining activities like observing, listening, speaking, writing, and drawing can help students to acquire, synthesize, and reinforce their knowledge of the world. In a field course, the senses of smell and even taste can also inform and enrich the educational experience. Smelling the twig of a black birch, the leaves of spicebush, the flowers of skunk cabbage, or the wonderful rotten-egg aroma of a salt marsh are ecological observations that lead to questions of “why?” and “how?” Furthermore, the sense of smell seems to be strongly linked to memory, albeit in poorly understood ways (i.e., the Proust effect). Incorporating these sorts of sensory experiences into laboratory and lecture-based courses is challenging. However, I recently discovered a laboratory activity that was developed to explicitly appeal to the students’ sense of smell. Well, perhaps “appeal” is the wrong word here. The activity nicely demonstrates some important aspects of wetland biogeochemistry, a topic that my wetland ecology students often struggle with, and it does this while providing some considerable olfactory “thrills.”

Setup of two experiments. Each experiment included six microcosms, flooded for different lengths of time. Six experiments were done in total, allowing us to assess the influence of sulfate and organic matter quality and quantity on biogeochemical changes induced by flooding.

The lab was developed for a soil science class by R.S. Dungan, B.D. Lee, and C. Amrhein. It can be downloaded here. A set of microcosms are created by the students, each containing a soil which is flooded for a different length of time. A simple gaslock is used to prevent oxygen from entering the microcosms. We used six microcosms, representing flooding durations of 20 minutes, 1 day, 7 days, 14 days, 21 days, and 35 days. In the original activity, the soils were amended with a small amount of gypsum (for a source of sulfate) and nitrogen-rich organic matter (alfalfa). Students then measure changes in dissolved oxygen, iron, nitrate, and the presence of hydrogen sulfide.

We modified and expanded the lab for an upper-level wetland science course. For example, we ran experiments with and without an added sulfate source, approximating the chemical environments of a salt marsh versus a freshwater wetland. Within each of these environments, we also tested the effect that organic matter quality and quantity had on the biogeochemical changes induced by flooding. To do this, one set of microcosms contained no added carbon (i.e., only the carbon that was present in the soil), one was amended with alfalfa (low carbon:nitrogen ratio), and one was amended with Sphagnum moss (high carbon:nitrogen ratio). In addition to measuring dissolved oxygen, iron, and nitrate, we also measured sulfate, redox potential, and pH. Changes in concentrations were plotted against time and redox potential.

Photographs of the microcosms, after 35 days, for the different experimental setups.

The results were fantastic, and some are summarized in the video and figures below. I learned a few things by doing this lab; in particular, I think that with a little practice I could estimate redox potential using only my nose. Certainly that would be a great skill for a wetland delineator to have!

The short video includes repeat photographs of a single flask, and provides a nice visual summary of the observed changes. Too bad you can’t send smells through the internet…

Figure showing all the data collected by the class, with concentrations plotted against redox potential measurements. Below are student comments along the redox potential gradient.

Biogeochemical changes with soil flooding, showing selected data from the class. Soils included a small amount of gypsum as a sulfate source, and the three lines indicate the results with organic matter of varying quality and quantity.

Biogeochemical changes with soil flooding, showing selected data from the class. No sulfate source was added, and the three lines indicate the results with organic matter of varying quality and quantity.

Questions for the students

A. Write a paragraph for each of the following questions, citing the appropriate figures:

Describe the sequence of biogeochemical changes that occured after soil flooding. What chemical transformations take place? Why do these changes occur?

Explain the observed differences between the experiments with and without the added sulfate source. Why did these differences occur? What implications do these results have for understanding energy flow in salt marshes and freshwater wetlands?

What is the likely effect of organic matter quality and quantity on the pattern and rate of biogeochemical changes after flooding? Why?

B. Write a sentence (or equations) for each of the following questions:

Hydrogen sulfide was produced in the experiment that reached a highly negative redox potential. What other gases were likely produced first?

What visual changes occurred in the experiment (added sulfate, low C:N) between day 15 and 20 (see video)? What caused these changes?

Why does nitrate increase in the first few days? What process is taking place?

If we allowed these experiments to continue longer, what gas might be released eventually?

I recently went to the Milwaukee Public Museum with my family. This destination was carefully chosen because they have a butterfly exhibit, and my 5-year old daughter has developed a butterfly obsession. In my experience, obsession of this sort is a good thing; in fact, it is the kind of thing that got me into science in the first place. After I proudly watched her carefully hold and observe the different species of butterflies, and even have a few pleasant conversations with them, I wandered the exhibit and observed the diversity of colors and shapes myself. There were some really spectacular species.

A butterfly amoeba

Perhaps because I recently had reason to open up Joseph Leidy’s incredibly beautiful 1879 foundational work describing North American testate amoebae (a group of amoebae that construct and live inside tests, or shells), my mind drifted to a statement Leidy made comparing a particular species of testate amoeba to a butterfly. Apparently the simple beauty and elegance of this particular testate amoeba caused him to radically change his research focus. He became obsessive about testate amoebae, or rhizopods as he called them. As with his previous research activities (e.g., paleontology, parisitology), his contributions to this new research area were enormous.

“No other lobose rhizopod has more impressed me with its beauty than this one. From its delicacy and transparency, its bright colors and form, as it moves among the leaves of sphagnum, desmids, and diatoms, I have associated it with the idea of a butterfly hovering among flowers.“

A portion of a plate from Joseph Leidy’s 1879 monograph showing some of his drawings of Hyalosphenia papilio….the butterfly amoeba.

Leidy notes that he first observed the species thirty years prior to the publication of his seminal work, and seeing the species brought him fond memories of his explorations in the New Jersey pine barrens:

“Upward of thirty years ago, while examining the structure of sphagnum, my attention was distracted by the movements of a singular animal, whose character and affinities I did not then recognize.”

“This interesting Rhizopod, together with a profusion of other remarkable microscopic forms of both animal and vegetal life, of which many are novel and yet undescribed, recalls pleasing recollections of excursions into the sphagnous bogs, cedar swamps, and pine barrens in the southern region of New Jersey.“

His fondness for the species is particularly evident in the next quote. I can’t help to laugh a bit at the image of him breaking out the microscope at a holiday dinner party, in order to display his “pets” to his friends. Perhaps I should try this the next time I host a lab get together!

“I have collected it from early spring to late autumn, and have retained it alive in sphagnum, in a glass case, through the winter. During the Christmas holidays, I have repeatedly exhibited it, in the living condition, to the admiration of friends.“

A portion of a plate from Leidy’s 1865 Cretaceous Reptiles of the United States, showing some vertebrae from Hadrosaurus. (Image source)

What I find most interesting about this, is that Leidy was 50 years old when he decided to pursue this new line research. He apparently dropped all of his other research endeavors, and focused solely on investigating these simple organisms for four or five years. This shift in research focus was made by an already famous man who described the first complete dinosaur fossil, as well as many other North American fossils, and was widely recognized as the leading expert in parasitology.

A drawing of Trichina spiralis (now Trichinella spiralis), the nematode parasite responsible for the disease trichinosis, done in 1887 by Joseph Leidy. Leidy first discovered that trichinosis was caused by a parasite that survived in undercooked meat (Chapman, 1891). Image source: Collection 532. Joseph Leidy Teaching Diagrams. Academy of Natural Sciences of Philadelphia.

His obituary in the Proceedings of the National Academy of Arts and Sciences suggests that he left his paleontological research because of the extreme rivalries and unfriendly arguments that were shaping the field at the time – rather than get involved in these controversies Leidy may have just moved on. He certainly would not be the only scientist to do such a thing. However, according to his own words, it was the beauty of Hyalosphenia papilio that led him to study testate amoebae:

“September 9th, 1873, the fiftieth anniversary of my birth, a friend, Clarence S. Bement, presented me with a Hartnack microscope, which, from its convenient size and form, I kept on my study table. From time to time I was led to make observations on Fresh-water Rhizopods detected in sediments collected in the vicinity of Philadelphia. A year later, in examining water squeezed from sphagnum obtained at Absecom, I observed many individuals of the same singular animal above indicated, but now, understanding its nature, I described it asDifflugia (Hyalosphenia) papilio. It was the rediscovery of this beautiful form which impelled me to pursue the investigations which constitute the material of the present work.”

Published in 1897, his “Freshwater Rhizopods of North America” is a stunning combination of science and art, and still the most exhaustive description of North American testate amoebae. For an interesting read on Leidy and the culture of science in mid-1800s North America, pick up a copy of Leonard Warren’s “Joseph Leidy: The last man who knew everything.” For more on Leidy and a wonderful online version of the drawings included in the 1879 masterpiece, go here and here.

Joseph Leidy with his microscope circa 1870.

Leaping the hedges

The idea of following one’s interests, wherever they take you, is very attractive to me. Of course, the culture of science has changed dramatically since the 1800s and scientists are generally narrower in focus and constrained by institutional expectations of tenure and promotion. However, Leidy’s path of scientific exploration still seems a natural one, and I suspect that if more scientists followed his model instead of obsessively chasing promotion or the next big grant, we would collectively learn more about the natural world.

When I interviewed for a faculty position one of the questions that I was asked was to describe my 5-year research plan. I was prepared for such a question, as it seemed like the sort of thing that I would be asked. In fact, I carefully designed my research talk (candidates in academia usually “interview” for several days, typically giving one or two public lectures) to incorporate aspects of my long-term research plan. Seven years later, perhaps not surprisingly, the most interesting science that I have done had little to do with my “plan.” The projects that have excited me the most have been the things that I or my students have stumbled upon…things that I never could have planned.

I sincerely doubt that Joesph Leidy had a plan. Sometimes something as simple as a beautiful amoeba, or a colorful butterfly, or perhaps an amoeba reminiscent of a butterfly…. can lead a scientist to wonderful new places. Hopefully they will lead a certain 5-year old girl to some interesting places too. The trick is identifying and following your passions (and obsessions), and knowing when it is time to move on to something new. Leidy knew both…and he said so in the concluding statements of his great work:

“”I may perhaps continue in the same field of research and give to the reader further results, but I cannot promise to do so; for though the subject has proved to me an unceasing source of pleasure, I see before me so many wonderful things in other fields that a strong impulse disposes me to leap the hedges to examine them.””

-rkb

Addendum:

After posting I ran into this great piece. A nice example of testate amoebae as inspiration for art.

What happens when a testate amoeba and a diatom get into a brawl? The testate amoeba wins of course. Below is a fun video of a testate amoeba spitting out a diatom – it has been up on youtube for quite a few years, but I happened to stumble across it today. The diatom is expelled at the very end…

Like this:

Peat mining at Minden Bog in Michigan. Minden Bog is probably the last true raised bog left in the state, and more than half of it has been mined. This picture was taken looking north from about the center of the bog, where peat mining was actively underway (Photo: R.K. Booth)

They are bug-infested wastelands. Wet and soggy places unfit for agricultural crops. Areas that should be made “useful” by drainage. Or at least those were the prevailing attitudes before the value of wetlands became widely recognized. In fact, government policies actively promoted the drainage of wetlands in the 1800s and much of the 1900s, with various incentive-based programs aimed at “reclaiming” swamps and other “overflowed” lands. Public funding was also provided for drainage activities. However, wetlands are now universally recognized as valuable providers of ecosystem services, playing critical roles in water purification, flood control, storm protection, nutrient removal from agricultural runoff, carbon storage, fishery support, and providing habitat for rare plants and animals. Thus, today many conservation agencies are actively working to identify, manage, protect, and restore wetlands. Many of these efforts are focused on the protection of systems that have been little impacted by human activities, or restoring degraded wetlands to a more natural state. Therefore, knowledge of how humans have impacted our remaining wetlands is critical to successful protection and restoration.

Drainage. Ditching. Filling. Extracting peat. These are some of the more obvious activities that damage or destroy these ecosystems. However, human activities also have indirect effects, such as ecological changes brought on by invasive species, changes in the acidity or chemistry of surface waters, changes in water levels due to groundwater use, and climate change. However, for some wetlands, there may be another indirect effect that has not been fully considered. Dust. Microscopic dust. Could something so small really have a big impact? We recently addressed this question by studying a bog in western Pennsylvania.

Sundew (Drosera sp.) is a carnivorous plant common to bogs and other nutrient-poor wetlands. A sticky substance, resembling dew in appearance, is released at the tip of each tentacle and traps small insects. The carnivorous habit allows the plant to supplement its nutrient intake. (Photo: R.K. Booth)

Dust, deforestation, and bogs

European settlers logged the vast majority of eastern North America about 100 to 150 years ago, substantially altering terrestrial ecosystems and the regional landscape. In many regions, widespread agriculture was established shortly after logging. Collectively, these activities increased soil-dust movement. Mobilization of dust would have occurred as cultivated fields replaced forests, and the treeless landscape would have allowed dust to move greater distances. This dust landed on adjacent ecosystems, including “wastelands” where agriculture was not possible…those soggy, bug-infested wetlands.

Bogs – a unique type of wetland characterized by very low nutrients – would be expected to be more sensitive to dust deposition than other wetland types. Why? Because the organisms that occur in bogs are adapted to low-nutrient availability. Carnivorous plants, which supplement their nutrient uptake by capturing small insects, are commonly found in bogs, and virtually all plants in bogs have some adaptation that allows them to survive in the nutrient-limited environment. Soil dust contains nitrogen, phosphorus, and other elements, so increasing dust deposition might actually fertilize the bog. You might think that this would be a good thing, as more fertilizer on your garden clearly makes for happier plants. However, on a bog it has the potential to change the outcome of competition among plants, alter microbial communities, and change the rates of important processes like decomposition and primary production. Changes in the relative rates of these processes would alter rates of peat accumulation – a fundamental property of these wetland ecosystems. But is the fertilization effect of dust enough to do these things? Can increased dust deposition cause the composition of bog plant communities to change? How about microbial communities? Is the impact of dust fertilization large enough to alter the relative rates of decomposition and primary production? Can enhanced dust deposition fundamentally change the bog ecosystem, including the ecosystem services it provides?

Titus Bog is surrounded by a nearly impenetrable shrub swamp, which made hauling the sediment-coring equipment to the site a bit of a challenge. (Photo: M.E. Sullivan)

The ecology of dust?

Alex Ireland carefully wraps up a portion of a peat core from Titus Bog, and prepares it for transport back to laboratory. (Photo: RK Booth)

Of course, in most regions of eastern North America, widespread deforestation occurred over a century ago, so to address our questions a retrospective approach was needed. Luckily, bogs preserve a record of past dust deposition and environmental conditions in the form of peat, which gradually accumulates in these environments. The acidic and oxygen-depleted environment within the peat is well-suited for the long-term preservation of plants and other organisms that occurred within and around the bog in the past. We carefully examined the paleoecological record from Titus Bog, a protected wetland in western Pennsylvania, to assess whether dust deposition increased at the time of deforestation, and if so, how this affected the bog. We collected a series of peat cores from the wetland, and used the information contained in these cores to reconstruct how the ecology of the bog has changed over the past several hundred years (Ireland & Booth 2012).

Conceptual model summarizing the ecological dynamics that likely resulted from the indirect effects of deforestation of the uplands surrounding Titus Bog in the late 1800s and early 1900s. From Ireland & Booth (2012).

Our results revealed that before European settlement, Titus Bog was a typical acidic bog, dominated by mosses that thrive in low-nutrient conditions. However, a layer of mineral dust marks the onset of big ecological changes in the peat cores. This mineral-rich layer contains pollen from agricultural weeds that expanded rapidly as Europeans converted forests to fields, allowing us to confidently link the increased dust deposition with human land clearance. Measurements of nutrient content of the peat revealed that the dust fertilized the surface of Titus Bog, and the increased nutrient availability led to changes in plant communities. In particular, it allowed woody plants to out-compete the mosses, shifting the relative abundance of these plant groups. As the plant communities were changing in response to increased nutrients, the microscopic organisms living on the wetland surface also changed, indicating that the dust deposition led to changes in multiple trophic levels. These changes in plant and microbial communities were also associated with increases in rates of decomposition, which may have altered the rate that the system performed one important ecosystem service – the sequestration of carbon dioxide from the atmosphere.

Today, much of the land south and east of Titus Bog is still used for agriculture, although a thin forest buffer exists between the agricultural fields and the wetland. (Photo: RK Booth)

Interestingly, the wetland that exists today is fundamentally different from the one that was present just a few hundred years ago, although the reestablishment of a thin forest buffer may be helping the system slowly recover. Our results highlight the importance of forest buffers, particularly upwind of bog environments, in the management of these systems. Things that are small and easy to overlook, like dust, can have big impacts. In the case bogs, successfully protection really may need to consider what is blowin’ in the wind.

White pines (Pinus strobus) growing on Titus Bog. The paleoecological record and tree-ring collections suggest that white pine became much more abundant on the bog after European deforestation of the upland (Ireland & Booth, 2012).

Should microbial biodiversity (i.e., microscopic organisms like bacteria, archea, protists, and some fungi) be more directly considered in conservation efforts? Certainly the importance of microscopic organisms in the earth system cannot be overstated, as they play vital roles in global element cycles – fixing atmospheric nitrogen and making it available to plants, returning nitrogen back to the atmosphere, playing important roles in food webs, and facilitating the decomposition of organic matter. Furthermore, microorganisms are likely to become a critical source for new pharmaceuticals in the future (Chivian & Bernstein, 2008). However, only rarely have microorganisms been included in biodiversity surveys, and although the International Union for Conservation of Nature (IUCN) recently added four critically endangered protists to the Red List (here, here, here, and here), a public outcry for their protection appears unlikely any time soon.

Of course the lack of emphasis on microorganisms in conservation biology is not particularly surprising, given that 1) we know relatively little about microbial diversity, 2) microbes are perhaps slightly less cute and charismatic than many other organism groups (although they are certainly cuter than some species), and 3) it has been widely assumed that microbial species have cosmopolitan distributions. In other words, they are found everywhere. More specifically, a microbial species occurs anywhere that suitable habitat exists for that particular species. In 1934, Baas Becking simply stated this hypothesis as: “everything is everywhere, but the environment selects” (de Wit and Bouvier 2006). What is implied by this hypothesis is that dispersal does not limit the distribution of microbes, and endemism (i.e., being confined to a particular region) should be rare. Of course, if everything is everywhere, then we don’t need to worry much about any particular microbial species, because extinction is extremely unlikely unless the destruction of all suitable habitats occurs…across the entire planet. Let’s hope that remains unlikely for some time.

However, research now clearly indicates that microbial biogeography is more nuanced and complex than implied by the “everything is everywhere” hypothesis. Many examples of limited geographic ranges have emerged over the past couple decades. Some particularly striking examples are within the testate amoebae, a group of shell-producing protists that have been relatively well studied, at least in comparison to many other microbial groups. For example, Apodera vas and species of the genus Certesella are restricted to the southern hemisphere and tropics, although suitable habitats for these species exist in Eurasia and North America (Smith and Wilkinson 2007). The patterns suggest that these species had their origins on the continent of Gondwana sometime after it separated from Laurasia about 200-180 million years ago, and thus their current distribution may be a reflection of this geological and evolutionary history (Smith and Wilkinson 2007). Apparently these species have been unable to disperse to North America or Eurasia.

A paleogeographic reconstruction of the Earth in the late Triassic, shortly before the separation of Gondwana (southern continents) from Laurasia (northern continents). The present distribution of Apodera vas and species of the genus Certesella is nearly restricted to the land that was once part of Gondwana, suggesting that they evolved on this landmass (Smith & Wilkinson 2007). (Image from wikipedia.org).

A potentially more restricted distribution pattern is that of Nebela ansata, an unusual (and dare I say, “charismatic”) species of testate amoebae known only from a few locations in eastern North America. In 1874, Joseph Leidy first encountered this species from collections he made in the New Jersey Pine Barrens (Leidy 1879). Since his initial descriptions, the species has only been recorded in the literature three times, always in temperate eastern North America, and always living in wetlands on moist Sphagnum moss. The species has gone unrecorded in the literature since the early 1950s, despite the intensive sampling of wetland testate amoeba communities (Heger et al. 2011).

The search for a forgotten microbe

Nebela ansata from Webb’s Mill Bog in the New Jersey Pine Barrens. The horn-like lateral extensions are characteristic for the species. (Photo: Thierry Heger)

The New Jersey Pine Barrens are only a few hours from Lehigh University, so a few years ago we set out to see if we could find Leidy’s elusive and long-forgotten microbe. His original samples were from cedar swamps near the town of Absecom (now spelled Absecon), and we used that as a guide when selecting potential wetlands for our sampling effort. He also mentioned that Nebela ansata was commonly found in association with Nebela carinata, a more widely distributed species. The ecology of Nebela carinata has been well characterized, and it prefers very wet Sphagnum moss and is often abundant where the water table is only a few centimeters below the moss surface. We used this knowledge to target likely habitats within each of the wetlands that we sampled. Maura Sullivan (Lehigh University, PhD student) and I sampled for two full days, returned the samples to the lab for examination, and managed to find the species!

Interesting, at about the same time as our rediscovery of Nebela ansata in the New Jersey Pine Barrens, the species was also discovered in Nova Scotia by Barry Warner and Taro Asada (University of Waterloo). A collaborative effort soon took shape, with the goal of pulling together all the known information on the distribution, ecology, and phylogeny of the species. Led by Thierry Heger, then a PhD student (Swiss Federal Research Institute WSL & The University of Geneva), an exhaustive literature and museum survey was undertaken and used in tandem with analyses of the samples from Nova Scotia and Pine Barrens to provide insight into the biogeography and ecology of Nebela ansata. Together, the the results provide a compelling case of a microorganism with a very limited distribution range – apparently limited to temperate, eastern North America – representing a very clear exception to the ‘everything is everywhere’ hypothesis (Heger et al. 2011).

Webb’s Mill wetland in the New Jersey Pine Barrens, where individuals of the rare testate amoeba species, Nebela ansata, were found.

How many other microorganisms also have geographically restricted distributions? What are the primary causes of these restricted distributions? How many endemic species remain undescribed? What role do these relatively rare microorganisms play in ecosystems? How many microbial species are vulnerable to habitat destruction or other global changes? Much work remains to be done in biodiversity research.